How samples are collected

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Today’s technologies allow testing on an impressively wide variety of samples (sometimes called specimens) that are collected from the human body. Most commonly these are blood, urine, saliva, sputum, faeces, semen and other bodily fluids, as well as tissue.

Urine, faeces, sputum & semen

Some samples such as urine, faeces, sputum, and semen can be easily collected by the patient. For many people, collecting the samples themselves is often the preferred way because of greater privacy but sometimes professional help is needed. These types of samples can be collected at home and brought to a medical practitioner's rooms or clinic or a pathology collection centre. When samples are collected professionally there is always someone on hand to help and to provide instructions. Experienced health professionals are well aware of the potential for embarrassment and often there are printed instructions on how to obtain samples – contaminated or badly collected samples can be unable to be tested in the laboratory.

Here are some examples of types of samples typically collected by the patient. It is very important that all instructions for sample collection are carefully followed. See Your Role Make sure you understand the instructions before collecting your sample. Requirements can vary between laboratories, hospitals and doctors.

Semen — Patients ejaculate into a specimen container. Usually, they need to refrain from ejaculating for 3 to 4 days before collecting the specimen. The specimen must be kept warm and brought to the lab within the time period specified.

Sputum — Patients are instructed to cough up sputum from as far down in the lungs as possible. (Some doctors prefer people to do this under professional guidance in the surgery.)

Stool — People usually collect this sample themselves during toileting. Instructions usually emphasise the importance of preventing the sample from becoming contaminated from other material in the toilet bowl and to wash their hands well after handling the sample. They may also be told to avoid certain foods during the test period. Depending on the test, they may be instructed to collect the sample into a container, scoop a small portion into a vial, or smear a small amount on special test paper.

Urine — Most urine specimens are collected by urinating into a container or receptacle. To keep the sample from becoming contaminated by materials outside the urinary tract, instructions are provided on how to clean the area. For some tests, a first-void urine sample is required. This is when the urine is at its most concentrated. Other tests require a mid-stream urine sample – after a small amount of urine has been passed. Collecting the urine specimen can be awkward. For certain tests, 24-hour urine samples are collected at home and may need to be refrigerated. It’s important to wash hands well after collecting the sample.

Saliva — This type of sample may be collected using a swab or, if a larger volume is needed for testing, by expectorating into a container.

Blood, swabs & bodily fluids

Blood — Samples can be collected from blood vessels (capillaries, veins, and sometimes arteries) by trained phlebotomists (usually pathology collectors or nurses). A fine needle is used and blood is withdrawn into a special collection tube. The procedure takes just a few minutes and can sting just a bit, typically when the needle is inserted or withdrawn. See Test tips & How it's done on blood collection .

Swabs – Many samples are collected by running a swab over an affected area. Procedures of this type can be collected by the patient or by a professional. The sample can be sent to a laboratory for analysis, although a few tests can provide immediate results in the doctor’s rooms. Throat, nasal, vaginal, and superficial wound cultures are obtained in this way. The procedures, while they occasionally can be uncomfortable, are generally quick, relatively painless and have no after-effects.

Samples from open wounds and sores — If a wound or sore is located in the outer layer of skin, the specimen is typically collected on a swab by brushing it over the area and gathering a sample of fluid or pus. Touching the open wound area may be temporarily painful since the wound is likely to be tender and sore. If a wound or infection is deep, however, a needle and syringe may be used to aspirate a sample of fluid or pus from the site.

Secretions and fluids from the nose or throat — Samples are collected by running a swab over the area. People typically respond to swabbing of their throat with a momentary gag reflex. If the throat is sore, the sample collection, brief as it is, can be uncomfortable. Similarly, a nasal swab may be a bit uncomfortable as the swab is inserted and reaches areas inside the nose that are typically never touched. It is a good idea to ask the practitioner or health professional if there are ways to minimise any soreness that may result. It can be helpful to perform relaxation techniques before, during, or after the procedure.

Secretions and tissues from the female reproductive system — Samples of vaginal secretions are obtained by running a cotton swab over the walls of the vagina. Also, cervical cells for a Pap smear are obtained using a special spatula or a tiny brush. Endometrial tissue samples are obtained by inserting a thin, flexible, hollow tube into the uterus, during which a slight pinch or brief cramping might be felt. It’s common for people to feel embarrassed and vulnerable because of how these samples are collected. A sensitive approach by the health care professional contributes greatly to a person’s emotional comfort. If you are physically uncomfortable, try asking for what you need (such as a smaller speculum). Also, if you would be more at ease if a woman performs these procedures ask your clinic for a female practitioner.

Biopsies, needle aspirations, surgery, CSF & bone marrow

Some samples can only be obtained by more invasive procedures conducted by specially-trained doctors, pathologists and other medical personnel.
Because of the nature of these collections techniques, some discomfort may be involved. Knowing what the procedure involves can help alleviate anxiety. For more on this, see Coping with test discomfort and anxiety.

Some common collections of this type include:

Tissue biopsy — Samples of bodily tissue can be obtained from various places in the body such as breast, lung or skin and, depending on the site, may involve varying degrees of invasiveness and pain or discomfort. The time required to perform the procedure and for recovery can also vary greatly. These procedures are conducted by medical practitioners, pathologists and occasionally other medical personnel who have specialist training. Biopsies can be collected using procedures such as:

Needle biopsy or aspiration — A needle is inserted into the site and cells or fluid are withdrawn using a syringe. A slight pinch may be felt at the site of needle insertion. Usually no recovery time is required, and slight discomfort may be experienced afterwards.

An open biopsy is a minor surgical procedure in which an incision is made and a portion of tissue is cut from the site. A closed biopsy is a procedure in which an incision is made (usually smaller than an open biopsy) and an instrument is inserted to help guide the surgeon to the appropriate site and to obtain the sample. These biopsies are usually performed in a doctor’s procedure room or hospital operating room. A local or general anaesthetic is used, depending on the procedure, to ensure the patient remains comfortable. Very occasionally, a general anaesthetic is needed.

Surgery – samples are also obtained during surgical procedures. These are called ‘frozen sections’ after the technique used: tissue is removed and frozen for dissection to allow immediate investigation. Samples taken this way can be used to give the surgeon preliminary diagnosis while the surgery is in progress. Samples are also removed and sent to the lab for more detailed analysis.

Cerebrospinal fluid (CSF) — A sample of cerebrospinal fluid is obtained by lumbar puncture, sometimes called a spinal tap. This is a specialised but relatively routine procedure. It is usually performed while the person is lying on his or her side in a curled up fetal position but may sometimes be performed in a sitting position. The back is cleaned with an antiseptic and a local anaesthetic is injected under the skin. A special needle is inserted through the skin, between two vertebrae, and into the spinal canal. The doctor collects a small amount of CSF in multiple sterile vials. Then the needle is withdrawn and a sterile dressing and pressure are applied to the puncture site. The patient will then be asked to lie quietly in a flat position, without lifting their head, for one or more hours to avoid a potential post-test spinal headache. The lumbar puncture procedure usually takes less than half an hour. For most people, it is a moderately uncomfortable to somewhat painful procedure. The most common sensation is a feeling of pressure when the needle is introduced. Let your doctor know if you experience a headache or any abnormal sensations, such as pain, numbness, or tingling in your legs, or pain at the puncture site.

Other body fluids such as synovial fluid, peritoneal fluid, pleural fluid and pericardial fluid are collected using procedures similar to that used for CSF in that they require aspiration of a sample of the fluid through a needle into a collection vessel, such as a syringe or specimen container. They often require some patient preparation, use of a local anaesthetic, and a resting period following sample collection. For details, see the descriptions for arthrocentesis, paracentesis, thoracentesis, and pericardiocentesis.

Bone marrow — The bone marrow aspiration and/or biopsy procedure is performed by a doctor, pathologist or other trained specialist. Both types of samples may be collected from the hip bone (pelvis), and marrow aspirations may be collected from the breastbone (sternum). In children, samples may also be collected from a vertebra in the back or from the thigh bone (femur). The most common collection site is the top ridge (iliac crest) of the hip bone. Some patients are given a mild sedative before the procedure, and then the patient is asked to lie down on his or her stomach or side for the collection and their lower body is draped with cloths so that only the area surrounding the site is exposed. The site is cleaned with an antiseptic such as iodine, and injected with a local anaesthetic. When the site has numbed, the doctor inserts a needle through the skin and into the bone. For an aspiration, the doctor attaches a syringe to the needle and pulls back on the plunger. This creates vacuum pressure and pulls a small amount of marrow into the syringe. For a bone marrow biopsy, the doctor uses a special needle that allows the collection of a core (a cylindrical sample) of bone and marrow. Even though the patient’s skin has been numbed, the patient may feel brief but uncomfortable pressure (pulling and/or pushing) sensations during these procedures. After the needle has been withdrawn, a sterile bandage is placed over the site and pressure is applied. The patient is then usually instructed to lie quietly until their blood pressure, heart rate, and temperature are normal, and then to keep the collection site dry and covered for about 48 hours.